Identifying common prognostic factors in genomic cancer studies: A novel index for censored outcomes

Background  

With the growing number of public repositories for high-throughput genomic data, it is of great interest to combine the results produced by independent research groups. Such a combination allows the identification of common genomic factors across multiple cancer types and provides new insights into the disease process. In the framework of the proportional hazards model, classical procedures, which consist of ranking genes according to the estimated hazard ratio or the p-value obtained from a test statistic of no association between survival and gene expression level, are not suitable for gene selection across multiple genomic datasets with different sample sizes. We propose a novel index for identifying genes with a common effect across heterogeneous genomic studies designed to remain stable whatever the sample size and which has a straightforward interpretation in terms of the percentage of separability between patients according to their survival times and gene expression measurements.     

Use of ATP bioluminescence measurements for the estimation of biomass during biological humification

Summary The development of the microflora during the humification of grape pulp has been investigated by the determination of ATP using the bioluminescence technique. Several extraction methods were tested including the use of dimethylsulphoxide, trichloroacetic acid, grinding and ultrasonification. Dimethylsulphoxide and ultrasonification for 15 sec appeared to be the most effective. The ATP extract was stabilized when it was mixed with 0.75 mM glycine, 4.4 mM Mg-EDTA, pH 7.5 and frozen. The relative error of the ATP assay by bioluminescence did not exceed 6.5%. This method allowed us to show that at least five distinct reproducible microbial phases exist during grape pulp humification. These results show that the microbial biomass changes noticeably and at distinct times during composting.     

Comparison of basic peptides- and lipid-based strategies for the delivery of splice correcting oligonucleotides

Expression of alternatively spliced mRNA variants at specific stages of development or in specific cells and tissues contributes to the functional diversity of the human genome. Aberrations in alternative splicing were found as a cause or a contributing factor to the development, progression, or maintenance of numerous diseases. The use of antisense oligonucleotides (ON) to modify aberrant expression patterns of alternatively spliced mRNAs is a novel means of potentially controlling such diseases. Oligonucleotides can be designed to repair genetic mutations, to modify genomic sequences in order to compensate for gene deletions, or to modify RNA processing in order to improve the effects of the underlying gene mutation. Steric block ON approach have proven to be effective in experimental model for various diseases. Here, we describe our experience in investigating two strategies for ON delivery: ON conjugation with basic peptides and lipid-based particulate system (lipoplex). Basic peptides or Cell Penetrating Peptides (CPP) such as the TAT-derived peptide appear to circumvent many problems associated with ON and drug delivery. This strategy may represent the next paradigm in our ability to modulate cell function and offers a unique avenue for the treatment of disease. Lipoplexes result from the intimate interaction of ON with cationic lipids leading to ON carrying particles able to be taken up by cells and to release ON in the cytoplasm. We have used as an experimental model the correction of a splicing alteration of the mutated β-globin intron causing thalassemia. Data on cell penetration and efficacy of correction of specific steric block ON delivered either by basic peptides or lipoplex are described. A comparison of the properties of both delivery systems is made respective to the use of this new class of therapeutic molecules.     

CD3/Ti gamma A: a functional gamma-receptor complex expressed on human peripheral lymphocytes

We have recently developed a mAb designated anti-Ti gamma A, which was found to immunoprecipitate from the well characterized CD3+ TCR alpha/beta- F6C7 fetal clone a CD3-associated disulfide-linked gamma-glycoprotein. This antibody recognizes approximately 3% of adult peripheral lymphocytes and delineates a CD2+ CD3+ TCR alpha/beta- CD4- NKH1- subset where expression of CD8 appears to vary widely from one individual to another. In the present study, we have used anti-Ti gamma A mAb to assess whether gamma-chains expressed on these adult lymphocytes are used as functional R. The two activities which have been associated thus far with TCR gamma+ cells, that is, IL-2-dependent proliferation and non-MHC-restricted cytotoxicity, were investigated here by using either resting or activated Ti gamma A+ lymphocytes. On the resting state, these cells (which appear as a very homogeneous population of granular lymphocytes) mediate little if any NK activity that could not be augmented by anti-Ti gamma A mAb. In contrast, after initial stimulation by PHA plus rIL-2 and subsequent culture in the presence of IL-2, activated Ti gamma A+ lymphocytes were strongly lytic against a series of conventional NK target cell lines. This cytotoxic function was either blocked or enhanced by anti-Ti gamma A mAb, depending upon experimental conditions. With respect to proliferation, it was possible to induce responses of resting Ti gamma A+ lymphocytes with antibody-coated CNBr beads only in the presence of exogenous IL-2, whereas, in culture, the same cells proliferated directly and secreted IL-2 after treatment by anti-Ti gamma A beads. Taken together, these data demonstrate that a major subset of circulating CD3+ TCR alpha/beta- lymphocytes use protein products of T cell gamma rearranging genes as functional R structures.     

Nested chromosomal fragmentation in yeast using the meganuclease I-Sce I: a new method for physical mapping of eukaryotic genomes.

We have developed a new method for the physical mapping of genomes and the rapid sorting of genomic libraries which is based on chromosome fragmentation by the meganuclease I-Sce I, the first available member of a new class of endonucleases with very long recognition sequences. I-Sce I allows complete cleavage at a single artificially inserted site in an entire genome. Sites can be inserted by homologous recombination using specific cassettes containing selectable markers or, at random, using transposons. This method has been applied to the physical mapping of chromosome XI (620 kb) of Saccharomyces cerevisi and to the sorting of a cosmid library. Our strategy has potential applications to various genome mapping projects. A set of transgenic yeast strains carrying the I-Sce I sites at various locations along a chromosome defines physical intervals against which new genes, DNA fragments or clones can be mapped directly by simple hybridizations.     

A protein of Halobacterium halobium immunologically related to the v-myc gene product

A 70 kDa protein of Halobacterium halobium cross-reacts with an antiserum directed against the v-myc gene product of the avian myelocytomatosis virus (MC29). This cross-reaction is in agreement with hybridization studies which indicate that H. halobium possesses DNA and RNA sequences homologous to the v-myc gene.     

A target structure for a series of human cloned natural killer cell lines is recognized by both anti-TNKtar and 4F2 monoclonal antibodies

It was shown recently that a surface antigen termed TNKtar was likely to serve as a target molecule for three distinct human NK clones expressing the same clonotypic determinant (termed NKTa) present on a 90 KD recognition structure. In the present studies, we investigated whether TNKtar and a previously described antigen termed 4F2 were related. Parallel immunoprecipitations from membrane lysates of the same cells showed that both anti-TNKtar and 4F2 Mab precipitate a heterodimeric structure which resolves as two bands of identical m.w. (40 and 80 KD) in SDS-PAGE analysis under reducing conditions. Sequential immunoprecipitations demonstrated that the two antibodies are directed at the same molecule. However, one antibody did not block subsequent binding of the other, and vice versa, suggesting that anti-TNKtar and 4F2 Mab are directed at two distinct epitopes of the molecule. Functionally, it was found that 4F2 Mab was able, as well as anti-TNKtar, to selectively block cytotoxic function of JT9 cloned cells. Furthermore, as reported previously for anti-TNKtar, 4F2 had no effect when additional NKTa-NK clones were used as effector cells in cytotoxicity assays. Finally, cold target inhibition assays were performed by using cold target cells precoated with either anti-TNKtar or 4F2 Mab. These experiments showed that preincubation of target cells with either antibody blocked their ability to compete with their radiolabeled counterpart. Such results further strengthen the hypothesis that the activation antigen recognized by both anti-TNKtar and 4F2 Mab serves as a specific target structure for NKTa+ NK active clones. We discuss the importance of previous data concerning the 4F2 molecule in light of this functional role, which had not been identified previously.     

Bufonid nucleocytoplasmic hybrids arrested at the early gastrula stage lack a fibronectin-containing fibrillar extracellular matrix

Summary Most hybrids betweenBufo bufo andB. calamita obtained by nuclear transplantation become arrested at the early gastrula stage. In both parental controls and the hybrid embryos, the presence and distribution of extracellular matrix was analysed with fluorescent wheat germ agglutinin and by immunolabelling with antibodies directed against fibronectin. InB. bufo andB. calamita gastrulae and in the few hybrids that complete gastrulation, the inner surface of the blastocoel roof is covered by a fibronectin-rich fibrillar matrix. In nucleocytoplasmic hybrids whose development was arrested at the gastrula stage, the fibronectin-containing extracellular matrix was either totally absent or poorly developed and disorganized.     

Human autologous rosettes. IV. Their relation with interleukin 2 activity production and natural killer cells in cancer patients

Peripheral blood lymphocytes (PBL) of solid-tumor-bearing cancer patients produced a lower interleukin 2 (IL-2) activity after lectin stimulation than did those from normal subjects. Moreover natural killer (NK) cell activity and autologous rosette forming (ARF) cell rate are found significantly correlated with IL-2 production in these patients. No direct relation is observed between ARF cell ratio and NK cell activity in a given patient. A central role for IL-2 in cancer patient immune dysfunctions is suggested. Two lines of pathogenetic mechanisms are documented. First, PBL exhibited cellular function defects, namely, autologous receptor expression, IL-2 production, and NK activity. Second, these dysfunctions involved, at least partly, plasma factors. The possibility of specific deficiency, (e.g., thymic factors) is not documented. Conversely it is demonstrated that patient plasma contain immunosuppressive factor(s) that block(s) IL-2 production and ARF cell expression. Involvement of ARF cell receptor in T-cell activation is discussed.     

Use of microcalorimetry for the characterization of marine metabolic activity at the water-sediment interface

Metabolic processes occurring at the sea-water-sediment interface were studied using a circulation flow microcalorimeter. A methodology was developed to characterize rapid and global changes in metabolism and energy flow, not easily detectable with reductionist approaches. Sea water was pumped continuously, 5–10 mm above the sediment, in experimental microcosms; a 100-μm filter prevented passage of meiofauna. This “circulating interface” was taken through the microcalorimeter and from there to an oxygen electrode, and was returned to the microcosm. The microcosms were experimentally eutrophicated using peptone (4 mg·ml ^?1). The relationship between heat production and oxygen tension in the circulating interface has been compared with ATP production, ¹⁴CO₂ and [¹⁴C]particulate matter turnovers. Initial heat steady-state production rises to a peak of 130 to 180 μW·ml^?1 in 6 to 8 h after peptone treatment. The microcalorimetric peak is closely correlated with ¹⁴CO₂ turnover and partially correlated with micro-events on the pO₂ curve. ATP concentration and particulate-¹⁴C turnover increase constantly and then stabilize, with the establishment of a new heat production steady state. The approach provides an indication of the temporal behaviour of complex mixtures of microorganisms and ciliates at the water-sediment interface, and gives holistic measurements of energy flow after induced perturbation (eutrophication) of the ecosystem. Although many problems remain to be solved in this field, it is shown here that flow microcalorimetric measurements can be used to monitor the effects of addition of reagents like pollutants and nutrients.